Table 1.

Summary of the MUE and RMSD, R² and Kendall's tau coefficient (τ) of the eight systems based on cycle closure ΔΔG values.

System	# of ligands	# of perturbations	FEP+/OPLS 2.1 (kcal/mol)				AMBER GPU-TI/AMBER FF14SB + GAFF (1.8) (kcal/mol)				Difference* (kcal/mol)
			MUE	RMSD	R2	τ	MUE	RMSD	R2	τ	MUE	RMSD
Thrombin	11	16	0.76	0.93	0.17	0.21	0.46	0.62	0.50	0.54	−0.30	−0.31
Tyk2	16	24	0.75	0.93	0.48	0.54	1.07	1.27	0.24	0.26	0.32	0.34
Jnk1	21	31	0.78	1.00	0.35	0.44	1.07	1.45	0.05	0.23	0.29	0.45
CDK2	16	25	0.91	1.11	0.15	0.30	0.97	1.13	0.35	0.46	0.06	0.02
PTP1B	23	49	0.89	1.22	0.43	0.55	1.06	1.40	0.35	0.51	0.17	0.18
BACE	36	58	0.84	1.03	0.37	0.36	1.20	1.47	0.27	0.31	0.36	0.44
MCL1	42	71	1.16	1.41	0.26	0.35	1.52	1.83	0.16	0.28	0.36	0.42
P38a	34	56	0.80	1.03	0.62	0.60	1.20	1.56	0.31	0.39	0.40	0.53
Overall	199	330	0.90	1.14	0.36	0.44	1.17	1.50	0.23	0.34	0.27	0.36

^*The difference is calculated as AMBER MUE or RMSD minus Schrodinger MUE or RMSD.